The code looks good and shows good programming flow to use logical index. It will be very lengthy to explain why the result shows in that way. Maybe, if you replace your last line of code with the three lines below, the result would make more sense to you.
You can check the value of every variable after every step to make sense of the size and value of the variable.
Lat = [-1 -1 -1 -1 -1;
-2 -2 -2 -2 -2;
-3 -3 -3 -3 -3;
-4 -4 -4 -4 -4;
-5 -5 -5 -5 -5];
Lon = [-50 -40 -30 -20 -10;
-50 -40 -30 -20 -10;
-50 -40 -30 -20 -10;
-50 -40 -30 -20 -10;
-50 -40 -30 -20 -10];
Data = [1 2 3 4 5;
6 7 8 9 10;
11 12 13 14 15;
16 17 18 19 20;
21 22 23 24 25];
intervaloLat = [-3.5, -1.5];
intervaloLon = [-35, -15];
latDentroDoIntervalo = Lat >= intervaloLat(1) & Lat <= intervaloLat(2)
lonDentroDoIntervalo = Lon >= intervaloLon(1) & Lon <= intervaloLon(2)
index=latDentroDoIntervalo & lonDentroDoIntervalo
Resultado = zeros(size(Data))
Resultado(index)=Data(index)
Or, you can do it this way. This only applies when your "selected area" is "square".
RowIndex=find(all(latDentroDoIntervalo,2))
ColIndex=find(all(lonDentroDoIntervalo,1))
Resultado=Data(RowIndex,ColIndex)
